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OzTrack

OzTrack is a free-to-use web-based platform for the analysis and visualisation of animal tracking data. It was developed for the Australian animal tracking community but can be used to determine, measure and plot home-ranges for animals anywhere in the world.

This software is copyright The University of Queensland.

This software is distributed under the GNU GENERAL PUBLIC LICENSE Version 2. See the COPYING file for detail.

Installing on Ubuntu

The following instructions have been tested on Ubuntu 13.04 and 13.10.

Setting up the database

Install PostgreSQL and PostGIS:

sudo apt-get install -y postgresql-9.1 postgresql-client-9.1 postgresql-9.1-postgis postgresql-contrib-9.1

Sort out PostgreSQL authentication:

--- /etc/postgresql/9.1/main/pg_hba.conf.1	2013-10-12 14:03:37.171531579 +1000
+++ /etc/postgresql/9.1/main/pg_hba.conf	2013-10-12 14:03:40.923531719 +1000
@@ -87,7 +87,7 @@
 # TYPE  DATABASE        USER            ADDRESS                 METHOD
 
 # "local" is for Unix domain socket connections only
-local   all             all                                     peer
+local   all             all                                     md5
 # IPv4 local connections:
 host    all             all             127.0.0.1/32            md5
 # IPv6 local connections:

sudo service postgresql reload

Setup the OzTrack database, including PostGIS and UUID module:

sudo -u postgres psql -c "create user oztrack with password 'changeme';"
sudo -u postgres psql -c "create database oztrack with owner oztrack;"
sudo -u postgres psql -d oztrack -f /usr/share/postgresql/9.1/contrib/postgis-1.5/postgis.sql
sudo -u postgres psql -d oztrack -f /usr/share/postgresql/9.1/contrib/postgis-1.5/spatial_ref_sys.sql
sudo -u postgres psql -d oztrack -c "alter table geometry_columns owner to oztrack;"
sudo -u postgres psql -d oztrack -c "alter table spatial_ref_sys owner to oztrack;"
sudo -u postgres psql -d oztrack -c "alter view geography_columns owner to oztrack;"
sudo -u postgres psql -d oztrack -c 'create extension "uuid-ossp";'

Installing Linux packages

Install the following packages:

  • libgdal-dev: required by rgdal R package.
  • libproj-dev: required by rgdal R package.
  • libxml2-dev: required by plotKML R package.
  • libnetcdf-dev, netcdf-bin: required by ncdf R package.
sudo apt-get install -y libgdal-dev libproj-dev libxml2-dev libnetcdf-dev netcdf-bin

Installing R (including Rserve and other packages)

RServe can be installed on the same machine as the Web application and/or on one or more other hosts. See the org.oztrack.conf.rserveHosts configuration property described below for how to identify these other hosts to the main server. The following instructions should only be applied to hosts that will run Rserve.

Install R, including r-base-dev for compiling/installing auxiliary R packages. OzTrack has been tested with R versions 2.15.2, 3.0.1, and 3.0.2.

sudo tee /etc/apt/sources.list.d/cran.list > /dev/null << EOF
deb http://cran.csiro.au/bin/linux/ubuntu $(lsb_release -s -c)/
EOF
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
sudo apt-get update
sudo apt-get install -y --no-install-recommends r-base-core r-base-dev

Install the R packages used by OzTrack, including Rserve. Note that the following command takes a while (e.g. 10 minutes) because it downloads, compiles, tests, and installs a large number of dependencies.

sudo R --no-save << EOF
install.packages(
    c(
        "Rserve",
        "sp",
        "ade4",
        "adehabitatHR",
        "adehabitatMA",
        "maptools",
        "shapefiles",
        "rgdal",
        "alphahull",
        "raster",
        "plyr",
        "spatstat",
        "Grid2Polygons",
        "RColorBrewer",
        "googleVis",
        "spacetime",
        "plotKML"
    ),
    repos='http://cran.csiro.au/'
)
EOF

The kftrack and ukfsst packages need to be downloaded and installed from files.

wget -P /tmp 'https://geolocation.googlecode.com/files/kftrack_0.70-x64.tar.gz'
wget -P /tmp 'https://geolocation.googlecode.com/files/ukfsst_0.3-x64.tar.gz'
sudo R --no-save << EOF
install.packages('/tmp/kftrack_0.70-x64.tar.gz', repos=NULL)
install.packages(c('date', 'ncdf'), repos='http://cran.csiro.au/')
install.packages('/tmp/ukfsst_0.3-x64.tar.gz', repos=NULL)
EOF

If Rserve is running on the same host as the Web application, it will be started automatically. To run Rserve on other hosts, place the following script in /etc/init/rserve.conf. If necessary, replace "ubuntu" on the setuid with the name of another non-root user.

description "Rserve"

start on runlevel [2345]
stop on runlevel [!2345]

setuid ubuntu

respawn

script
R --no-save --slave > /dev/null 2>&1 <<EOF
library(Rserve)
run.Rserve(interactive='no', remote='enable')
EOF
end script

The service will start automatically at boot but can be started at other times using sudo service rserve start.

Installing Tomcat

Install Tomcat.

sudo apt-get install -y tomcat7

Configure ports for HTTP and HTTPS. The following assumes there's a reverse proxy that listens on ports 80/443 and terminates SSL. See Apache installation/config below.

--- /etc/tomcat7/server.xml.1   2013-11-06 16:17:00.813980000 +1000
+++ /etc/tomcat7/server.xml     2013-11-13 16:55:40.444228660 +1000
@@ -72,7 +72,8 @@
     <Connector port="8080" protocol="HTTP/1.1"
                connectionTimeout="20000"
                URIEncoding="UTF-8"
-               redirectPort="8443" />
+               redirectPort="8443"
+               proxyPort="80" />
     <!-- A "Connector" using the shared thread pool-->
     <!--
     <Connector executor="tomcatThreadPool"
@@ -90,6 +92,16 @@
                clientAuth="false" sslProtocol="TLS" />
     -->
 
+    <!-- Assmes there is a reverse proxy out front that handles SSL and
+         sends us traffic on ports 8080/8443 for HTTP/HTTPS respectively. -->
+    <Connector port="8443" protocol="HTTP/1.1"
+               connectionTimeout="20000"
+               URIEncoding="UTF-8"
+               SSLEnabled="false"
+               scheme="https"
+               secure="true"
+               proxyPort="443" />
+
     <!-- Define an AJP 1.3 Connector on port 8009 -->
     <!--
     <Connector port="8009" protocol="AJP/1.3" redirectPort="8443" />

Installing GeoServer

GeoServer is an open-source GIS server used to render map layers in OzTrack. OzTrack has been tested with GeoServer version 2.3.1. For complete installation instructions, see the GeoServer user manual.

The following commands install the GeoServer WAR distribution to Tomcat:

wget 'http://downloads.sourceforge.net/geoserver/geoserver-2.3.1-war.zip' -P /tmp/
sudo apt-get install -y unzip
unzip -d /tmp/geoserver /tmp/geoserver-2.3.1-war.zip
sudo service tomcat7 stop
sudo unzip -d /var/lib/tomcat7/webapps/geoserver/ /tmp/geoserver/geoserver.war
sudo chown -R tomcat7: /var/lib/tomcat7/webapps/geoserver/
sudo service tomcat7 start

Log in to the GeoServer web administation interface at http://localhost:8080/geoserver/web/ using the default username/password, "admin"/"geoserver", and follow the instructions for configuring security.

Installing Apache

The following commands install the Apache HTTP server and configure reverse proxying from port 80 to port 8080. Configuring HTTPS is optional and requires that you create and install an SSL certificate. Note that you should modify the ServerName directive and port numbers to match your deployment. Depending on your installation of Apache, you may need to place site configuration in either /etc/apache2/sites-available/oztrack.conf or /etc/apache2/sites-available/oztrack.

sudo apt-get install -y apache2
sudo a2enmod proxy_http
sudo service apache2 restart
sudo tee /etc/apache2/sites-available/oztrack.conf > /dev/null << EOF
<VirtualHost _default_:80>
  ServerName oztrack.org
  ProxyPreserveHost on
  ProxyPass /geoserver http://localhost:8080/geoserver nocanon retry=0
  ProxyPassReverse /geoserver http://localhost:8080/geoserver
  ProxyPass / http://localhost:8080/ nocanon retry=0
  ProxyPassReverse / http://localhost:8080/
</VirtualHost>

<VirtualHost _default_:443>
  ServerName https://oztrack.org
  SSLEngine on
  SSLCertificateFile /etc/apache2/ssl/oztrack.crt
  SSLCertificateKeyFile /etc/apache2/ssl/oztrack.key
  ProxyPreserveHost on
  ProxyPass /geoserver http://localhost:8443/geoserver nocanon retry=0
  ProxyPassReverse /geoserver http://localhost:8443/geoserver
  ProxyPass / http://localhost:8443/ nocanon retry=0
  ProxyPassReverse / http://localhost:8443/
</VirtualHost>
EOF
sudo a2ensite oztrack
sudo service apache2 reload

Installing Shibboleth

Install Apache with Shibboleth modules.

sudo apt-get install apache2 libapache2-mod-shib2

Enable SSL and Shibboleth modules.

sudo a2enmod ssl
sudo a2enmod shib2 
sudo service apache2 restart

Download AAF metadata signing certificate (either AAF Test Federation or AAF Production Federation).

sudo wget https://ds.test.aaf.edu.au/distribution/metadata/aaf-metadata-cert.pem -O /etc/shibboleth/aaf-metadata-cert.pem
sudo wget https://ds.aaf.edu.au/distribution/metadata/aaf-metadata-cert.pem -O /etc/shibboleth/aaf-metadata-cert.pem

Create service provider certificate

sudo /etc/shibboleth/keygen.sh -f -o /etc/shibboleth -h oztrack.org -e https://oztrack.org/shibboleth

Configure Shibboleth with Entity ID, Discovery Service, and Metadata Provider values matching your application and the AAF by editing /etc/shibboleth/shibboleth2.xml.

--- /etc/shibboleth/shibboleth2.xml.1   2013-11-07 11:13:28.293980000 +1000
+++ /etc/shibboleth/shibboleth2.xml     2013-11-07 11:58:01.557980000 +1000
@@ -20,7 +20,7 @@
     -->
 
     <!-- The ApplicationDefaults element is where most of Shibboleth's SAML bits are defined. -->
-    <ApplicationDefaults entityID="https://sp.example.org/shibboleth"
+    <ApplicationDefaults entityID="https://oztrack.org/shibboleth"
                          REMOTE_USER="eppn persistent-id targeted-id">
 
         <!--
@@ -40,8 +40,7 @@
             (Set discoveryProtocol to "WAYF" for legacy Shibboleth WAYF support.)
             You can also override entityID on /Login query string, or in RequestMap/htaccess.
             -->
-            <SSO entityID="https://idp.example.org/shibboleth"
-                 discoveryProtocol="SAMLDS" discoveryURL="https://ds.example.org/DS/WAYF">
+            <SSO discoveryProtocol="SAMLDS" discoveryURL="https://ds.test.aaf.edu.au/discovery/DS">
               SAML2 SAML1
             </SSO>
 
@@ -83,6 +82,12 @@
         <MetadataProvider type="XML" file="partner-metadata.xml"/>
         -->
 
+        <MetadataProvider type="XML" uri="https://ds.test.aaf.edu.au/distribution/metadata/metadata.aaf.signed.complete.xml"
+             backingFilePath="metadata.aaf.xml" reloadInterval="7200">
+           <MetadataFilter type="RequireValidUntil" maxValidityInterval="2419200"/>
+           <MetadataFilter type="Signature" certificate="aaf-metadata-cert.pem"/>
+        </MetadataProvider>
+
         <!-- Map to extract attributes from SAML assertions. -->
         <AttributeExtractor type="XML" validate="true" path="attribute-map.xml"/>

Uncomment attribute map elements by editing /etc/shibboleth/attribute-map.xml.

--- /etc/shibboleth/attribute-map.xml.1 2013-11-07 11:12:10.317980000 +1000
+++ /etc/shibboleth/attribute-map.xml   2013-11-07 11:12:40.877980000 +1000
@@ -52,7 +52,6 @@
     </Attribute>
 
     <!-- Some more eduPerson attributes, uncomment these to use them... -->
-    <!--
     <Attribute name="urn:mace:dir:attribute-def:eduPersonPrimaryAffiliation" id="primary-affiliation">
         <AttributeDecoder xsi:type="StringAttributeDecoder" caseSensitive="false"/>
     </Attribute>
@@ -75,10 +74,8 @@
 
     <Attribute name="urn:oid:1.3.6.1.4.1.5923.1.6.1.1" id="eduCourseOffering"/>
     <Attribute name="urn:oid:1.3.6.1.4.1.5923.1.6.1.2" id="eduCourseMember"/>
-    -->
 
     <!--Examples of LDAP-based attributes, uncomment to use these... -->
-    <!--
     <Attribute name="urn:mace:dir:attribute-def:cn" id="cn"/>
     <Attribute name="urn:mace:dir:attribute-def:sn" id="sn"/>
     <Attribute name="urn:mace:dir:attribute-def:givenName" id="givenName"/>
@@ -132,6 +129,5 @@
     <Attribute name="urn:oid:2.5.4.11" id="ou"/>
     <Attribute name="urn:oid:2.5.4.15" id="businessCategory"/>
     <Attribute name="urn:oid:2.5.4.19" id="physicalDeliveryOfficeName"/>
-    -->
 
 </Attributes>

Configure Apache by adding these lines to /etc/apache2/sites-available/oztrack.conf.

<Location />
  ShibRequestSetting authType shibboleth
  ShibRequestSetting requireSession false
  require shibboleth
  AuthType shibboleth
  ShibUseHeaders on
</Location>
 
<Location /login/shibboleth>
  ShibRequestSetting authType shibboleth
  ShibRequestSetting requireSession true
  require shibboleth
  AuthType shibboleth
  ShibUseHeaders on
</Location>

Restart all the services.

sudo service shibd restart
sudo service tomcat7 restart
sudo service apache2 restart

Installing OzTrack

OzTrack can be compiled from source into a WAR file by running mvn package.

The OzTrack WAR file can be run using any Java Servlet container.

Alternatively, it can be run as a normal Java application via the org.oztrack.app.OzTrackJettyServer class.

Configuring OzTrack

OzTrack can be configured via a range of properties. The properties files included in the distribution under /WEB-INF/classes/org/oztrack/conf/ contain default settings.

To override these default values, you have three options (in increasing order of precedence):

  • edit the /WEB-INF/classes/org/oztrack/conf/custom.properties file included in the distribution;
  • point to an external properties file using the org.oztrack.conf.customConfigFile system property;
  • override individual properties via Java system properties.

An advantage of pointing to an external configuration file rather than editing the custom.properties file included in the distribution is that you can keep configuration separate to the application, avoiding the need to apply patches each time a new version of the application is deployed.

System properties can be set as arguments to the java command (e.g. -Dorg.oztrack.conf.customConfigFile=/var/local/oztrack/custom.properties). When deploying to Tomcat, arguments can be added to the JAVA_OPTS variable used in the startup script.

The following are key properties that should be configured for all applications:

# Base URL for application, minus trailing slash.
org.oztrack.conf.baseUrl=http://localhost
# Directory used to store tracking data files.
# Ensure that this directory exists and can be written to by the application.
org.oztrack.conf.dataDir=/var/local/oztrack
# Username for PostgreSQL database.
org.oztrack.conf.databaseUsername=oztrack
# Password for PostgreSQL database.
org.oztrack.conf.databasePassword=changeme
# Username for Geoserver admin user.
org.oztrack.conf.geoServerUsername=admin
# Password for GeoServer admin user.
org.oztrack.conf.geoServerPassword=changeme
# SMTP host name for sending mail notifications.
org.oztrack.conf.mailServerHostName=smtp.example.org
# SMTP host port number for sending mail notifications.
org.oztrack.conf.mailServerPort=25
# Name in From field for mail notifications.
org.oztrack.conf.mailFromName=OzTrack
# Email address in From field for mail notifications.
[email protected]
# Date from which the ability to create closed access projects is disabled.
org.oztrack.conf.closedAccessDisableDate=2013-01-18T17:00:00
# Date from which project embargoes must be annually renewed.
org.oztrack.conf.nonIncrementalEmbargoDisableDate=2013-05-28T09:00:00
# Rserve hosts to connect to for running R analyses
org.oztrack.conf.rserveHosts=localhost,127.0.0.1
# Number of Rserve processes to run on each host
org.oztrack.conf.numRConnections=4

Administering OzTrack

OzTrack defines a default admin user with the username/password "admin"/"oztrack". To log into OzTrack, click the 'Login' button at the top-right of screen. You should change the default admin password immediately by selecting 'Edit profile' from within the user menu at the top-right of screen.

The admin user, unlike ordinary users in OzTrack, also has a 'Settings' link under the user menu; the settings page allows various aspects of the OzTrack application to be configured.

Installing external environmental layers

The environmental data layers included in OzTrack come from external sources and are covered by specific licence agreements. Due to their large file size and licencing restrictions, layer files are not packaged with OzTrack and must be obtained under a new licence agreement by parties deploying their own instance of OzTrack. Note that OzTrack can be run without these layers but their associated menu items in the map interface won't do anything when clicked.

GEBCO (bathymetry, elevation)

The GEBCO_08 Grid (30 arc-second interval) is distributed in NetCDF format as gebco_08.nc. For compatibility with GeoServer, we convert this to GeoTIFF format using the following command:

gdal_translate -of GTiff gebco_08.nc gebco_08.tif

The resulting file should be placed in $GEOSERVER_HOME/coverages/gebco_08/gebco_08.tif.

National Dynamic Land Cover Dataset

The Dynamic Land Cover Dataset is distributed in GeoTIFF format.

Files contained in the distribution (DLCDv1_Class.tif, DLCDv1_Class.tif.xml, etc) should be placed under $GEOSERVER_HOME/coverages/DLCDv1_Class/.

National Vegetation Information System

The NVIS layers are distributed in Arc/Info Binary Grid format. For compatibility with GeoServer, we convert them to GeoTIFF format using the following commands:

gdal_translate \
-a_srs EPSG:3577 \
-of GTiff \
GRID_NVIS4_1_AUST_MVG_EXT/aust4_1e_mvg/hdr.adf \
nvis_4_1_aust_mvg.tif

gdal_translate \
-a_srs EPSG:3577 \
-of GTiff \
GRID_NVIS4_1_AUST_MVG_EXT/aust4_1e_mvg/hdr.adf \
nvis_4_1_aust_mvs.tif

The resulting file should be placed in $GEOSERVER_HOME/coverages/nvis_4_1_aust_mvg/nvis_4_1_aust_mvg.tif and $GEOSERVER_HOME/coverages/nvis_4_1_aust_mvs/nvis_4_1_aust_mvs.tif.

Fire Frequency

The Fire Frequency layer is distributed in Arc/Info Binary Grid format. For compatibility with GeoServer, we convert it to GeoTIFF format using the following command:

gdal_translate -of GTiff fire-frequency-avhrr-1997-2009 fire-frequency-avhrr-1997-2009.tif

The resulting files should be placed in $GEOSERVER_HOME/coverages/fire-frequency-avhrr-1997-2009/fire-frequency-avhrr-1997-2009.tif and $GEOSERVER_HOME/coverages/fire-frequency-avhrr-1997-2009/fire-frequency-avhrr-1997-2009.tif.aux.xml.

Collaborative Australian Protected Areas Database (land)

The CAPAD layers are distributed in Shapefile format. To simplify layer management in OzTrack, we merge the capad10_external and capad10_external_restricted Shapefiles into a single Shapefile using the open-source QGIS application. In QGIS, select Vector > Data Management Tools > Merge shapefiles and enter the paths for the two Shapefiles.

The resulting files should be placed under $GEOSERVER_HOME/shapefiles/capad10_external_all/.

Collaborative Australian Protected Areas Database (marine)

The CAPAD layers are distributed in Shapefile format. To simplify layer management in OzTrack, we merge the capad10_m_external and capad10_m_external_restricted Shapefiles into a single Shapefile using the open-source QGIS application. In QGIS, select Vector > Data Management Tools > Merge shapefiles and enter the paths for the two Shapefiles.

The resulting files should be placed under $GEOSERVER_HOME/shapefiles/capad10_m_external_all/.

Commonwealth Marine Reserves Network

The Commonwealth Marine Research Network layer is distributed in Shapefile format.

Files contained in the distribution should be placed under $GEOSERVER_HOME/shapefiles/commonwealth_marine_reserves_network_2012/.

Natural Resource Management (NRM) Regions

The NRM Regions layer is distributed in Shapefile format.

Files contained in the distribution should be placed under $GEOSERVER_HOME/shapefiles/NRM_Regions_2010/.

Interim Biogeographic Regionalisation for Australia (IBRA)

The IBRA layers are distributed in Shapefile format.

Files contained in the distribution should be placed under $GEOSERVER_HOME/shapefiles/IBRA7_regions/ and $GEOSERVER_HOME/shapefiles/IBRA7_subregions/.

Integrated Marine and Coastal Regionalisation of Australia (IMCRA)

The IMCRA layers are distributed in Shapefile format.

Files contained in the distribution should be placed under $GEOSERVER_HOME/shapefiles/imcra_mesoscale_bioregions/ and $GEOSERVER_HOME/shapefiles/imcra_provincial_bioregions/.

CSIRO Atlas of Regional Seas (CARS)

The CARS layers are distributed in NetCDF format, with longitudes between 0 and 360 degrees. For compatibility with GeoServer, we need to convert to GeoTIFF format and shift coordinates to be -180 to 180 degrees.

The following script converts from NetCDF and creates two GeoTIFF files for each layer - one to the east and one to the west of the prime meridian - then merges them together so the resulting image spans -180 to 180.

#!/bin/bash

function f() {
    gdalinfo NETCDF:"${1}.nc":mean | grep -A5 'Corner Coordinates'
    echo

    gdalinfo NETCDF:"${1}.nc":mean | grep -A11 '^Band 1\>'
    echo

    gdal_translate \
        -projwin -0.25 90.25 180.25 -75.25 \
        -a_ullr  -0.25 90.25 180.25 -75.25 \
        -a_srs 'EPSG:4326' \
        -b 1 \
        -of GTiff \
        NETCDF:${1}.nc:mean \
        /tmp/${2}_east.tif

    gdal_translate \
        -projwin  179.75 90.25 359.75 -75.25 \
        -a_ullr  -180.25 90.25  -0.25 -75.25 \
        -a_srs 'EPSG:4326' \
        -b 1 \
        -of GTiff \
        NETCDF:${1}.nc:mean \
        /tmp/${2}_west.tif

    gdal_merge.py \
        -o /tmp/${2}.tif \
        /tmp/${2}_west.tif \
        /tmp/${2}_east.tif

    rm \
        /tmp/${2}_west.tif \
        /tmp/${2}_east.tif

    echo
}


f nitrate_cars2009 cars2009_nitrate
f oxygen_cars2009 cars2009_oxygen
f phosphate_cars2009 cars2009_phosphate
f salinity_cars2009a cars2009a_salinity
f silicate_cars2009 cars2009_silicate
f temperature_cars2009a cars2009a_temperature
f hgt2000_cars2009a cars2009a_hgt2000

The resulting files should be placed in $GEOSERVER_HOME/coverages/cars2009_nitrate/cars2009_nitrate.tif, $GEOSERVER_HOME/coverages/cars2009_oxygen/cars2009_oxygen.tif, $GEOSERVER_HOME/coverages/cars2009_phosphate/cars2009_phosphate.tif, $GEOSERVER_HOME/coverages/cars2009a_salinity/cars2009a_salinity.tif, $GEOSERVER_HOME/coverages/cars2009_silicate/cars2009_silicate.tif, $GEOSERVER_HOME/coverages/cars2009a_temperature/cars2009a_temperature.tif, $GEOSERVER_HOME/coverages/cars2009a_hgt2000/cars2009a_hgt2000.tif.

Configuring GeoServer layers

OzTrack automatically creates and updates layers in GeoServer. To configure layers in GeoServer, log in to OzTrack as admin, click the 'GeoServer' link on the Settings page, and click the 'Update GeoServer' button. Any errors encountered updating GeoServer will be listed on the response page; in particular, you will see errors if creation of external environmental layers fail due to missing layer files.

Developer notes

Upgrading jQuery UI theme

The jQuery UI theme used on this project is produced using the jQuery UI ThemeRoller (http://jqueryui.com/themeroller/). To modify the theme, use the link included in the ThemeRoller-generated CSS file to pre-fill settings in the theme creation form.

grep 'jqueryui\.com\/themeroller\/?' src/main/webapp/css/jquery-ui/*.css

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Web application for uploading, viewing and analysing animal tracking data

oztrack.org/

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